^Since the winner of the 2016–17 Estonian Cup FCI Tallinn had qualified to Champions League, the cup winners' spot was inherited by forth-placed club Flora.

Relegation play-offs

At season's end Pärnu, the ninth place club, participated in a two-legged play-off with Maardu Linnameeskond, the runners-up (of independent teams) of the 2016 Esiliiga, for the spot in 2017 Meistriliiga.[27]

Source: Estonian Football Association1 ^ The home team is listed in the left-hand column.2 ^ EJL awarded Flora a win due to Narva Trans fielding a suspended player. The original match had ended in a 0–2 defeat.Colours: Blue = home team win; Yellow = draw; Red = away team win.